YBOX3_RAT
ID YBOX3_RAT Reviewed; 361 AA.
AC Q62764; Q63748;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 25-MAY-2022, entry version 137.
DE RecName: Full=Y-box-binding protein 3;
DE AltName: Full=Cold shock domain-containing protein A;
DE AltName: Full=DNA-binding protein A;
DE AltName: Full=Muscle Y-box protein YB2;
DE AltName: Full=RYB-A;
DE AltName: Full=Y-box-binding protein A;
GN Name=Ybx3; Synonyms=Csda, Dbpa, Yb2;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Sprague-Dawley;
RA Goldman D., Gao J., Burmeister M., Sapru M.;
RT "Characterization of muscle Y-box proteins that bind the nAChR delta
RT subunit promoter.";
RL Submitted (MAR-1995) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Wistar; TISSUE=Liver;
RX PubMed=8029009; DOI=10.1093/nar/22.11.2036;
RA Ito K., Tsutsumi K., Kuzumaki T., Gomez P.F., Otsu K., Ishikawa K.;
RT "A novel growth-inducible gene that encodes a protein with a conserved
RT cold-shock domain.";
RL Nucleic Acids Res. 22:2036-2041(1994).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2; SER-33; SER-52; SER-193;
RP SER-195; SER-196; SER-335; SER-358 AND SER-359, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Binds to the GM-CSF promoter. Seems to act as a repressor.
CC Binds also to full-length mRNA and to short RNA sequences containing
CC the consensus site 5'-UCCAUCA-3'. May have a role in translation
CC repression (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Found in a mRNP complex with YBX2. Interacts with RRP1B.
CC {ECO:0000250|UniProtKB:P16989, ECO:0000250|UniProtKB:Q9JKB3}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Comment=Additional isoforms seem to exist.;
CC Name=1;
CC IsoId=Q62764-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q62764-2; Sequence=VSP_001137;
CC -!- TISSUE SPECIFICITY: Abundant in the skeletal muscle, spleen and fetal
CC liver.
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DR EMBL; U22893; AAB60520.1; -; mRNA.
DR EMBL; D28557; BAA05907.1; -; mRNA.
DR PIR; S51608; S51608.
DR RefSeq; NP_114185.3; NM_031979.3. [Q62764-1]
DR AlphaFoldDB; Q62764; -.
DR SMR; Q62764; -.
DR BioGRID; 249842; 1.
DR IntAct; Q62764; 3.
DR MINT; Q62764; -.
DR STRING; 10116.ENSRNOP00000007427; -.
DR iPTMnet; Q62764; -.
DR PhosphoSitePlus; Q62764; -.
DR jPOST; Q62764; -.
DR PaxDb; Q62764; -.
DR PRIDE; Q62764; -.
DR GeneID; 83807; -.
DR KEGG; rno:83807; -.
DR UCSC; RGD:621056; rat. [Q62764-1]
DR CTD; 8531; -.
DR RGD; 621056; Ybx3.
DR eggNOG; KOG3070; Eukaryota.
DR InParanoid; Q62764; -.
DR OrthoDB; 1431946at2759; -.
DR PhylomeDB; Q62764; -.
DR PRO; PR:Q62764; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISO:RGD.
DR GO; GO:0005921; C:gap junction; IDA:MGI.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0003677; F:DNA binding; ISO:RGD.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; ISO:RGD.
DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR GO; GO:1905538; F:polysome binding; ISO:RGD.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; ISO:RGD.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; ISO:RGD.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:RGD.
DR GO; GO:0031100; P:animal organ regeneration; IEP:RGD.
DR GO; GO:0071474; P:cellular hyperosmotic response; ISO:RGD.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; ISO:RGD.
DR GO; GO:0009566; P:fertilization; ISO:RGD.
DR GO; GO:0001701; P:in utero embryonic development; ISO:RGD.
DR GO; GO:0008584; P:male gonad development; ISO:RGD.
DR GO; GO:0043066; P:negative regulation of apoptotic process; ISO:RGD.
DR GO; GO:1902219; P:negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress; ISO:RGD.
DR GO; GO:0060546; P:negative regulation of necroptotic process; ISO:RGD.
DR GO; GO:0048642; P:negative regulation of skeletal muscle tissue development; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:RGD.
DR GO; GO:0046622; P:positive regulation of organ growth; ISO:RGD.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0007283; P:spermatogenesis; IEP:RGD.
DR CDD; cd04458; CSP_CDS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR019844; CSD_1.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; CSD_1; 1.
DR PROSITE; PS51857; CSD_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Cytoplasm; DNA-binding; Methylation;
KW Nucleus; Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT CHAIN 2..361
FT /note="Y-box-binding protein 3"
FT /id="PRO_0000100216"
FT DOMAIN 85..149
FT /note="CSD"
FT REGION 1..73
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 173..361
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 22..38
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 2
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 33
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 52
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 126
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 193
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 195
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 196
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 243
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 313
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 315
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 335
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 358
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 359
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT VAR_SEQ 184..252
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_001137"
FT CONFLICT 14
FT /note="L -> H (in Ref. 2; BAA05907)"
FT /evidence="ECO:0000305"
FT CONFLICT 52..74
FT /note="SPGGDAAPGPAPASSAPAGSEDA -> APARASPRARPGLISPRGKRGR
FT (in Ref. 2; BAA05907)"
FT /evidence="ECO:0000305"
FT CONFLICT 120..121
FT /note="PR -> HV (in Ref. 2; BAA05907)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 361 AA; 38852 MW; C6799D5A3DA5C3F3 CRC64;
MSEAGEATTG GTTLPQAAAD APAAAPPDPA PKSPAASGAP QAPAPAALLA GSPGGDAAPG
PAPASSAPAG SEDAEKKVLA TKVLGTVKWF NVRNGYGFIN RNDTKEDVFV HQTAIKKNNP
RKYLRSVGDG ETVEFDVVEG EKGAEAANVT GPDGVPVEGS RYAADRRRYR RGYYGRRRGP
PRNYAGEEEE EGSGSSEGFE PPAADGQFSG ARNQLRRPQY RPPYRQRRFP PYHVGQTFDR
RSRVFPHPNR MQAGEIGEMK DGVPEGAQLQ VHRNPTYRPR FRRGPARPRP APAIGEAEDK
ENQQAANGPN QPSARRGFRR PYNYRRRPRP LNAVSQDGKE TKAGEAPTEN PAPATEQSSA
E
